Numerous residues, such as the coffee pulp, are generated throughout coffee processing. This by-product is a source of antioxidant phytochemicals, including phenolic compounds and caffeine. However, the antioxidant properties of the phenolic compounds from the coffee pulp are physiologically limited to their bioaccessibility, bioavailability, and biotransformation occurring during gastrointestinal digestion. Hence, this study explored the phenolic and caffeine profile in the coffee pulp flour (CPF) and extract (CPE), their intestinal bioaccessibility through in vitro digestion, and their potential bioavailability and colonic metabolism using in silico models. The CPE exhibited a higher concentration of phenolic compounds than the CPF, mainly phenolic acids (protocatechuic, chlorogenic, and gallic acids), followed by flavonoids, particularly quercetin derivatives. Caffeine was found in higher concentrations than phenolic compounds. The antioxidant capacity was increased throughout the digestive process. The coffee pulp matrix influenced phytochemicals’ behavior during gastrointestinal digestion. Whereas individual phenolic compounds generally decreased during digestion, caffeine remained stable. Then, phenolic acids and caffeine were highly bioaccessible, while flavonoids were mainly degraded. As a result, caffeine and protocatechuic acid were the main compounds absorbed in the intestine after digestion. Non-absorbed phenolic compounds might undergo colonic biotransformation yielding small and potentially more adsorbable phenolic metabolites. These results contribute to establishing the coffee pulp as an antioxidant food ingredient since it contains bioaccessible and potentially bioavailable phytochemicals with potential health-promoting properties.